Chromosome fusions, common in cancer cells, result from telomere loss at chromosome ends (Liu, Cheng, & Hsieh, 2009). Complicated to grasp mechanistically, these fusions may result in aberrant gene products as well as prevent deterioration and cleavage of chromosome isoforms (Wang et al., submitted). Currently, the ciliate Oxytricha trifallax holds the record for the most fragments during the fragmentation process in conjugation. Oxytricha is capable of separating into an 8-gene nanochromosome (Swart et al., 2013). The research presented in this thesis discovers the robustness of piRNA injection to induce chromosome fusions and the influential role that these small oligonucleotides play in the origin of multi-gene chromosomes. O. trifallax has been pushed to form a 5-gene isoform via triggering the fusion of three adjacent chromosomes from a single MIC locus by microinjections of 27 nt piRNAs. Fusions assayed by PCR showed a viable triple fusion of the MAC DNA of contigs 11682.0, 20527.0, and 16348.0; however, fusions assayed by Southern analysis only confirmed a double fusion of contigs 20527.0 and 16348.0 when probed with contig20527.0. Nonetheless, the linkage of 5 genes was accomplished representing novel research for the strength of piRNAs in ciliate systems such as Oxytricha. Therefore, piRNAs act as mediators in the linkage of adjacent genes in MIC DNA while protecting DNA sequences from aberrant breakages or deletions.